Pinned Repositories
cuttlefish
Building the compacted de Bruijn graph efficiently from references or reads.
kmers
A bit-packed k-mer representation (and relevant utilities) for rust
perplexity
pufferfish2
seine-rs
A (rust)🦀 library and suite of tools for manipulating and processing the output of salmon, alevin, and alevin-fry 🐟
EMF
kmers
A bit-packed k-mer representation (and relevant utilities) for rust
PySigProfiler
Python implementation of SigProfiler
simple-sds
Simple succinct data structures (in Rust)
snakemake-tutorial
theJasonFan's Repositories
theJasonFan/kmers
A bit-packed k-mer representation (and relevant utilities) for rust
theJasonFan/simple-sds
Simple succinct data structures (in Rust)
theJasonFan/chacon
Commitable HAsh CONtracts.
theJasonFan/cuttlefish
Building the compacted de Bruijn graph efficiently from references or reads.
theJasonFan/KMC
Fast and frugal disk based k-mer counter
theJasonFan/advent-of-code-2020
theJasonFan/bamgineer
Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
theJasonFan/CMSC828O
theJasonFan/cmsc858D
Succinct data structures for CMSC858D
theJasonFan/criterion.rs
Statistics-driven benchmarking library for Rust
theJasonFan/dotfiles
theJasonFan/gradual-typing
Implementation of Gradually Typed Lambda Calculus
theJasonFan/jf.zsh-theme
theJasonFan/kelp
Contig tiling to reference sequence simulator
theJasonFan/mazu-pybindings
Testing out python bindings for mazu default indexes
theJasonFan/meta-review
Manuscript describing open collaborative writing with Manubot
theJasonFan/metagraph-workflows
theJasonFan/nf-tower-aws
Repository containing required policies for Nextflow Tower deployment on AWS
theJasonFan/nf-wc
`wc` from Nextflow, can be useful for testing deployments
theJasonFan/pufferfish
An efficient index for the colored, compacted, de Bruijn graph
theJasonFan/pufferfish2
theJasonFan/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
theJasonFan/rust-boomphf
Fast and scalable minimal perfect hashing for massive key sets
theJasonFan/rust-clippy
A bunch of lints to catch common mistakes and improve your Rust code
theJasonFan/scanpy
Single-cell analysis in Python. Scales to >1M cells.
theJasonFan/SEQC-data
Download SEQC data - aggregate reads for replicates across flowcellls and sites - rename samples with usable names
theJasonFan/shoal
Improved multi-sample transcript abundance estimates using adaptive priors
theJasonFan/umd-thesis-template
theJasonFan/umdcs-prelim-approval
theJasonFan/yay-evil-emacs
😈 A lightweight literate Emacs config with even better "better defaults". Shipped with a custom theme!